GenomeNet

Database: UniProt
Entry: Q9LSV0
LinkDB: Q9LSV0
Original site: Q9LSV0 
ID   GLYR1_ARATH             Reviewed;         289 AA.
AC   Q9LSV0; B9DFS5; F4J913; Q94A74; Q94B07;
DT   06-FEB-2013, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   16-JAN-2019, entry version 136.
DE   RecName: Full=Glyoxylate/succinic semialdehyde reductase 1;
DE            Short=AtGLYR1;
DE            Short=AtGR1;
DE            Short=SSA reductase 1;
DE            EC=1.1.1.79 {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
DE            EC=1.1.1.n11 {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
DE   AltName: Full=Gamma-hydroxybutyrate dehydrogenase {ECO:0000303|PubMed:12882961};
DE            Short=AtGHBDH;
GN   Name=GLYR1; Synonyms=GR1; OrderedLocusNames=At3g25530;
GN   ORFNames=MWL2.18;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND FUNCTION.
RC   STRAIN=cv. Landsberg erecta;
RX   PubMed=12882961; DOI=10.1074/jbc.M305717200;
RA   Breitkreuz K.E., Allan W.L., Van Cauwenberghe O.R., Jakobs C.,
RA   Talibi D., Andre B., Shelp B.J.;
RT   "A novel gamma-hydroxybutyrate dehydrogenase: identification and
RT   expression of an Arabidopsis cDNA and potential role under oxygen
RT   deficiency.";
RL   J. Biol. Chem. 278:41552-41556(2003).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA   Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT   features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT   clones.";
RL   DNA Res. 7:131-135(2000).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana
RT   reference genome.";
RL   Plant J. 89:789-804(2017).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC   STRAIN=cv. Columbia;
RX   PubMed=14593172; DOI=10.1126/science.1088305;
RA   Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   STRAIN=cv. Columbia;
RX   PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA   Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M.,
RA   Seki M., Shinozaki K.;
RT   "Analysis of multiple occurrences of alternative splicing events in
RT   Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL   DNA Res. 16:155-164(2009).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC   STRAIN=cv. Columbia;
RA   Shinn P., Chen H., Kim C.J., Ecker J.R.;
RT   "Arabidopsis ORF clones.";
RL   Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases.
RN   [7]
RP   FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RA   Hoover G.J., Van Cauwenberghe O.R., Breitkreuz K.E., Clark S.M.,
RA   Merrill A.R., Shelp B.J.;
RT   "Characteristics of an Arabidopsis glyoxylate reductase: general
RT   biochemical properties and substrate specificity for the recombinant
RT   protein, and developmental expression and implications for glyoxylate
RT   and succinic semialdehyde metabolism in planta.";
RL   Can. J. Bot. 85:883-895(2007).
RN   [8]
RP   FUNCTION, CATALYTIC ACTIVITY, AND KINETIC PARAMETERS.
RA   Hoover G.J., Prentice G.A., Merrill A.R., Shelp B.J.;
RT   "Kinetic mechanism of a recombinant Arabidopsis glyoxylate reductase:
RT   studies of initial velocity, dead-end inhibition and product
RT   inhibition.";
RL   Can. J. Bot. 85:896-902(2007).
RN   [9]
RP   SUBCELLULAR LOCATION.
RX   PubMed=18495639; DOI=10.1093/jxb/ern123;
RA   Simpson J.P., Di Leo R., Dhanoa P.K., Allan W.L., Makhmoudova A.,
RA   Clark S.M., Hoover G.J., Mullen R.T., Shelp B.J.;
RT   "Identification and characterization of a plastid-localized
RT   Arabidopsis glyoxylate reductase isoform: comparison with a cytosolic
RT   isoform and implications for cellular redox homeostasis and aldehyde
RT   detoxification.";
RL   J. Exp. Bot. 59:2545-2554(2008).
RN   [10]
RP   INDUCTION.
RX   PubMed=18495640; DOI=10.1093/jxb/ern122;
RA   Allan W.L., Simpson J.P., Clark S.M., Shelp B.J.;
RT   "Gamma-hydroxybutyrate accumulation in Arabidopsis and tobacco plants
RT   is a general response to abiotic stress: putative regulation by redox
RT   balance and glyoxylate reductase isoforms.";
RL   J. Exp. Bot. 59:2555-2564(2008).
RN   [11]
RP   INDUCTION BY OZONE.
RX   PubMed=19453511; DOI=10.1111/j.1399-3054.2009.01220.x;
RA   Yoshida S., Tamaoki M., Ioki M., Ogawa D., Sato Y., Aono M., Kubo A.,
RA   Saji S., Saji H., Satoh S., Nakajima N.;
RT   "Ethylene and salicylic acid control glutathione biosynthesis in
RT   ozone-exposed Arabidopsis thaliana.";
RL   Physiol. Plantarum 136:284-298(2009).
RN   [12]
RP   SUBCELLULAR LOCATION.
RX   PubMed=22309191; DOI=10.1111/j.1744-7909.2012.01103.x;
RA   Ching S.L., Gidda S.K., Rochon A., van Cauwenberghe O.R., Shelp B.J.,
RA   Mullen R.T.;
RT   "Glyoxylate reductase isoform 1 is localized in the cytosol and not
RT   peroxisomes in plant cells.";
RL   J. Integr. Plant Biol. 54:152-168(2012).
RN   [13]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22223895; DOI=10.1074/mcp.M111.015131;
RA   Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C.,
RA   Meinnel T., Giglione C.;
RT   "Comparative large-scale characterisation of plant vs. mammal proteins
RT   reveals similar and idiosyncratic N-alpha acetylation features.";
RL   Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN   [14]
RP   X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS).
RA   Hoover G., Jorgensen R., Merrill A.R., Shelp B.J.;
RT   "Cytosolic NADPH-dependent glyoxylate reductase from Arabidopsis:
RT   crystal structure and kinetic characterization of active site
RT   mutants.";
RL   Submitted (JUL-2008) to the PDB data bank.
CC   -!- FUNCTION: Catalyzes the NADPH-dependent reduction of glyoxylate to
CC       glycolate as well as succinic semialdehyde (SSA) to gamma-
CC       hydroxybutyrate in vitro. May function in redox homeostasis and
CC       play a role in oxidative stress tolerance by detoxifying
CC       glyoxylate and SSA generated in glycolate metabolism and GABA
CC       metabolism, respectively. {ECO:0000269|PubMed:12882961,
CC       ECO:0000269|Ref.7, ECO:0000269|Ref.8}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=glycolate + NADP(+) = glyoxylate + H(+) + NADPH;
CC         Xref=Rhea:RHEA:10992, ChEBI:CHEBI:15378, ChEBI:CHEBI:29805,
CC         ChEBI:CHEBI:36655, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349;
CC         EC=1.1.1.79; Evidence={ECO:0000269|Ref.7, ECO:0000269|Ref.8};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=4-hydroxybutanoate + NADP(+) = H(+) + NADPH + succinate
CC         semialdehyde; Xref=Rhea:RHEA:26381, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:16724, ChEBI:CHEBI:57706, ChEBI:CHEBI:57783,
CC         ChEBI:CHEBI:58349; EC=1.1.1.n11; Evidence={ECO:0000269|Ref.7,
CC         ECO:0000269|Ref.8};
CC   -!- ACTIVITY REGULATION: The ratio of NADPH/NADP(+) may regulate
CC       enzymatic activity. {ECO:0000305}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=4.5 uM for glyoxylate {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
CC         KM=870 uM for succinate semialdehyde {ECO:0000269|Ref.7,
CC         ECO:0000269|Ref.8};
CC         KM=2.2 uM for NADPH (in the presence of glyoxylate as
CC         cosubstrate) {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
CC         KM=2.6 uM for NADPH (in the presence of succinate semialdehyde
CC         as cosubstrate) {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
CC       {ECO:0000269|PubMed:18495639, ECO:0000269|PubMed:22309191}.
CC       Note=According to PubMed:22309191, GLYR1 does not localize in the
CC       peroxisome as initially described in PubMed:18495639.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q9LSV0-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q9LSV0-2; Sequence=VSP_045054;
CC         Note=No experimental confirmation available.;
CC   -!- INDUCTION: By salinity, drought, submergence, cold and heat
CC       stresses, and ozone. {ECO:0000269|PubMed:18495640,
CC       ECO:0000269|PubMed:19453511}.
CC   -!- MISCELLANEOUS: Follows a sequentially ordered Bi-Bi catalytic
CC       mechanism involving the complexation of NADPH to the enzyme before
CC       glyoxylate or SSA, and the release of NADP(+) before glycolate or
CC       gamma-hydroxybutyrate, respectively. Although GLYR1 acts as an
CC       aldo/keto reductase, it has no significant homology with either
CC       mammalian and bacterial NADPH-dependent SSA reductases.
CC   -!- SIMILARITY: Belongs to the HIBADH-related family. NP60 subfamily.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAK83640.1; Type=Frameshift; Positions=227; Evidence={ECO:0000305};
DR   EMBL; AY044183; AAK94781.1; -; mRNA.
DR   EMBL; AB025639; BAB01322.1; -; Genomic_DNA.
DR   EMBL; CP002686; AEE77021.1; -; Genomic_DNA.
DR   EMBL; CP002686; AEE77022.1; -; Genomic_DNA.
DR   EMBL; AY049298; AAK83640.1; ALT_FRAME; mRNA.
DR   EMBL; AK316884; BAH19592.1; -; mRNA.
DR   EMBL; BT025039; ABE02414.1; -; mRNA.
DR   RefSeq; NP_001030765.1; NM_001035688.1. [Q9LSV0-2]
DR   RefSeq; NP_566768.1; NM_113449.4. [Q9LSV0-1]
DR   UniGene; At.21370; -.
DR   PDB; 3DOJ; X-ray; 2.10 A; A=1-289.
DR   PDBsum; 3DOJ; -.
DR   ProteinModelPortal; Q9LSV0; -.
DR   SMR; Q9LSV0; -.
DR   BioGrid; 7470; 1.
DR   STRING; 3702.AT3G25530.1; -.
DR   iPTMnet; Q9LSV0; -.
DR   PaxDb; Q9LSV0; -.
DR   PRIDE; Q9LSV0; -.
DR   ProMEX; Q9LSV0; -.
DR   EnsemblPlants; AT3G25530.1; AT3G25530.1; AT3G25530. [Q9LSV0-1]
DR   EnsemblPlants; AT3G25530.2; AT3G25530.2; AT3G25530. [Q9LSV0-2]
DR   GeneID; 822139; -.
DR   Gramene; AT3G25530.1; AT3G25530.1; AT3G25530. [Q9LSV0-1]
DR   Gramene; AT3G25530.2; AT3G25530.2; AT3G25530. [Q9LSV0-2]
DR   KEGG; ath:AT3G25530; -.
DR   Araport; AT3G25530; -.
DR   TAIR; locus:2094518; AT3G25530.
DR   eggNOG; KOG0409; Eukaryota.
DR   eggNOG; COG2084; LUCA.
DR   HOGENOM; HOG000219608; -.
DR   KO; K18121; -.
DR   OMA; NRTLAKC; -.
DR   OrthoDB; 812358at2759; -.
DR   PhylomeDB; Q9LSV0; -.
DR   BioCyc; ARA:AT3G25530-MONOMER; -.
DR   BioCyc; MetaCyc:MONOMER-10405; -.
DR   BRENDA; 1.1.1.26; 399.
DR   BRENDA; 1.1.1.61; 399.
DR   BRENDA; 1.1.1.79; 399.
DR   EvolutionaryTrace; Q9LSV0; -.
DR   PRO; PR:Q9LSV0; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   ExpressionAtlas; Q9LSV0; baseline and differential.
DR   Genevisible; Q9LSV0; AT.
DR   GO; GO:0005829; C:cytosol; IDA:TAIR.
DR   GO; GO:0003858; F:3-hydroxybutyrate dehydrogenase activity; IMP:TAIR.
DR   GO; GO:0030267; F:glyoxylate reductase (NADP) activity; IEA:UniProtKB-EC.
DR   GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR   GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR   GO; GO:0006979; P:response to oxidative stress; IMP:TAIR.
DR   Gene3D; 1.10.1040.10; -; 1.
DR   InterPro; IPR002204; 3-OH-isobutyrate_DH-rel_CS.
DR   InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR   InterPro; IPR013328; 6PGD_dom2.
DR   InterPro; IPR006115; 6PGDH_NADP-bd.
DR   InterPro; IPR015815; HIBADH-related.
DR   InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR   InterPro; IPR029154; NADP-bd.
DR   Pfam; PF14833; NAD_binding_11; 1.
DR   Pfam; PF03446; NAD_binding_2; 1.
DR   PIRSF; PIRSF000103; HIBADH; 1.
DR   SUPFAM; SSF48179; SSF48179; 1.
DR   SUPFAM; SSF51735; SSF51735; 1.
DR   PROSITE; PS00895; 3_HYDROXYISOBUT_DH; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Acetylation; Alternative splicing; Complete proteome;
KW   Cytoplasm; NAD; NADP; Oxidoreductase; Reference proteome;
KW   Stress response.
FT   CHAIN         1    289       Glyoxylate/succinic semialdehyde
FT                                reductase 1.
FT                                /FTId=PRO_0000421032.
FT   NP_BIND       4     18       NADP. {ECO:0000250|UniProtKB:Q49A26}.
FT   ACT_SITE    170    170       {ECO:0000250}.
FT   BINDING      95     95       NADP. {ECO:0000250|UniProtKB:Q49A26}.
FT   BINDING     238    238       NADP. {ECO:0000250|UniProtKB:Q49A26}.
FT   MOD_RES       1      1       N-acetylmethionine.
FT                                {ECO:0000244|PubMed:22223895}.
FT   VAR_SEQ      73     83       Missing (in isoform 2).
FT                                {ECO:0000303|PubMed:19423640}.
FT                                /FTId=VSP_045054.
FT   CONFLICT    223    223       N -> T (in Ref. 1; AAK94781).
FT                                {ECO:0000305}.
FT   CONFLICT    263    263       A -> V (in Ref. 5; BAH19592).
FT                                {ECO:0000305}.
FT   STRAND        2      6       {ECO:0000244|PDB:3DOJ}.
FT   HELIX        10     21       {ECO:0000244|PDB:3DOJ}.
FT   STRAND       25     29       {ECO:0000244|PDB:3DOJ}.
FT   HELIX        33     36       {ECO:0000244|PDB:3DOJ}.
FT   HELIX        37     41       {ECO:0000244|PDB:3DOJ}.
FT   HELIX        50     56       {ECO:0000244|PDB:3DOJ}.
FT   STRAND       58     62       {ECO:0000244|PDB:3DOJ}.
FT   HELIX        67     75       {ECO:0000244|PDB:3DOJ}.
FT   HELIX        80     83       {ECO:0000244|PDB:3DOJ}.
FT   STRAND       89     92       {ECO:0000244|PDB:3DOJ}.
FT   HELIX        98    110       {ECO:0000244|PDB:3DOJ}.
FT   STRAND      114    117       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       124    129       {ECO:0000244|PDB:3DOJ}.
FT   STRAND      132    138       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       140    153       {ECO:0000244|PDB:3DOJ}.
FT   STRAND      154    159       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       165    193       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       198    207       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       213    223       {ECO:0000244|PDB:3DOJ}.
FT   STRAND      230    232       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       233    249       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       255    269       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       277    280       {ECO:0000244|PDB:3DOJ}.
FT   HELIX       281    285       {ECO:0000244|PDB:3DOJ}.
SQ   SEQUENCE   289 AA;  30692 MW;  3E67002A19706636 CRC64;
     MEVGFLGLGI MGKAMSMNLL KNGFKVTVWN RTLSKCDELV EHGASVCESP AEVIKKCKYT
     IAMLSDPCAA LSVVFDKGGV LEQICEGKGY IDMSTVDAET SLKINEAITG KGGRFVEGPV
     SGSKKPAEDG QLIILAAGDK ALFEESIPAF DVLGKRSFYL GQVGNGAKMK LIVNMIMGSM
     MNAFSEGLVL ADKSGLSSDT LLDILDLGAM TNPMFKGKGP SMNKSSYPPA FPLKHQQKDM
     RLALALGDEN AVSMPVAAAA NEAFKKARSL GLGDLDFSAV IEAVKFSRE
//
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